Advances in Intelligent and Soft Computing 74 - Bisite
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Advances in Intelligent and Soft Computing Editor-in-Chief: J. Kacprzyk 74 Advances in Intelligent and Soft Computing Editor-in-Chief Prof. Janusz Kacprzyk Systems Research Institute Polish Academy of Sciences ul. Newelska 6 01-447 Warsaw Poland E-mail: [email protected] Further volumes of this series can be found on our homepage: springer.com Vol. 58. J. Mehnen, A. Tiwari, M. Köppen, A. Saad (Eds.) Applications of Soft Computing, 2009 ISBN 978-3-540-89618-0 Vol. 59. K.A. Cyran, S. Kozielski, J.F. Peters, U. Stańczyk, A. Wakulicz-Deja (Eds.) Man-Machine Interactions, 2009 ISBN 978-3-642-00562-6 Vol. 60. Z.S. Hippe, J.L. Kulikowski (Eds.) Human-Computer Systems Interaction, 2009 ISBN 978-3-642-03201-1 Vol. 61. W. Yu, E.N. Sanchez (Eds.) Advances in Computational Intelligence, 2009 ISBN 978-3-642-03155-7 Vol. 62. B. Cao, T.-F. Li, C.-Y. Zhang (Eds.) Fuzzy Information and Engineering Volume 2, 2009 ISBN 978-3-642-03663-7 Vol. 63. Á. Herrero, P. Gastaldo, R. Zunino, E. Corchado (Eds.) Computational Intelligence in Security for Information Systems, 2009 ISBN 978-3-642-04090-0 Vol. 66. G.Q. Huang, K.L. Mak, P.G. Maropoulos (Eds.) Proceedings of the 6th CIRP-Sponsored International Conference on Digital Enterprise Technology, 2009 ISBN 978-3-642-10429-9 Vol. 67. V. Snášel, P.S. Szczepaniak, A. Abraham, J. Kacprzyk (Eds.) Advances in Intelligent Web Mastering - 2, 2010 ISBN 978-3-642-10686-6 Vol. 68. V.-N. Huynh, Y. Nakamori, J. Lawry, M. Inuiguchi (Eds.) Integrated Uncertainty Management and Applications, 2010 ISBN 978-3-642-11959-0 Vol. 69. E. Pi˛etka and J. Kawa (Eds.) Information Technologies in Biomedicine, 2010 ISBN 978-3-642-13104-2 Vol. 70. XXX Vol. 71. XXX Vol. 72. J.C. Augusto, J.M. Corchado, P. Novais, C. Analide (Eds.) Ambient Intelligence and Future Trends, 2010 ISBN 978-3-642-13267-4 Vol. 64. E. Tkacz, A. Kapczynski (Eds.) Internet – Technical Development and Applications, 2009 ISBN 978-3-642-05018-3 Vol. 73. J.M. Corchado, P. Novais, C. Analide, J. Sedano (Eds.) Soft Computing Models in Industrial and Environmental Applications, 5th International Workshop (SOCO 2010), 2010 ISBN 978-3-642-13160-8 Vol. 65. E. Kacki, ˛ M. Rudnicki, J. Stempczyńska (Eds.) Computers in Medical Activity, 2009 ISBN 978-3-642-04461-8 Vol. 74. M.P. Rocha, F.F. Riverola, H. Shatkay, J.M. Corchado (Eds.) Advances in Bioinformatics ISBN 978-3-642-13213-1 Miguel P. Rocha, Florentino Fernández Riverola, Hagit Shatkay, and Juan Manuel Corchado (Eds.) Advances in Bioinformatics 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010) ABC Editors Miguel P. Rocha Dep. Informática / CCTC Universidade do Minho Campus de Gualtar 4710-057 Braga Portugal Hagit Shatkay Computational Biology and Machine Learning Lab School of Computing Queen’s University Kingston Ontario K7L 3N6 Canada E-mail: [email protected] Florentino Fernández-Riverola Escuela Superior de Ingeniería Informática Edificio Politécnico, Despacho 408 Campus Universitario As Lagoas s/n 32004 Ourense Spain E-mail: [email protected] Juan Manuel Corchado Departamento de Informática y Automática Facultad de Ciencias Universidad de Salamanca Plaza de la Merced S/N 37008 Salamanca Spain E-mail: [email protected] ISBN 978-3-642-13213-1 e-ISBN 978-3-642-13214-8 DOI 10.1007/978-3-642-13214-8 Advances in Intelligent and Soft Computing ISSN 1867-5662 Library of Congress Control Number: Applied For c 2010 Springer-Verlag Berlin Heidelberg This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable for prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Typeset & Cover Design: Scientific Publishing Services Pvt. Ltd., Chennai, India. Printed on acid-free paper 543210 springer.com Preface The fields of Bioinformatics and Computational Biology have been growing steadily over the last few years boosted by an increasing need for computational techniques that can efficiently handle the huge amounts of data produced by the new experimental techniques in Biology. This calls for new algorithms and approaches from fields such as Data Integration, Statistics, Data Mining, Machine Learning, Optimization, Computer Science and Artificial Intelligence. Also, new global approaches, such as Systems Biology, have been emerging replacing the reductionist view that dominated biological research in the last decades. Indeed, Biology is more and more a science of information needing tools from the information technology field. The interaction of researchers from different scientific fields is, more than ever, of foremost importance and we hope this event will contribute to this effort. IWPACBB'10 technical program included a total of 30 papers (26 long papers and 4 short papers) spanning many different sub-fields in Bioinformatics and Computational Biology. Therefore, the technical program of the conference will certainly be diverse, challenging and will promote the interaction among computer scientists, mathematicians, biologists and other researchers. We would like to thank all the contributing authors, as well as the members of the Program Committee and the Organizing Committee for their hard and highly valuable work. Their work has helped to contribute to the success of the IWAPCBB’10 event. IWPACBB’10 wouldn’t exist without your contribution. Miguel Rocha Florentino Fdez-Riverola IWPACBB’10 Organizing Co-chairs Juan Manuel Corchado Hagit Shatkay IWPACBB’10 Programme Co-chairs Organization General Co-chairs Miguel Rocha Florentino Riverola Juan M. Corchado Hagit Shatkay University of Minho (Portugal) University of Vigo (Spain) University of Salamanca (Spain) Queens University, Ontario (Canada) Program Committee Juan M. Corchado (Co-chairman) Alicia Troncoso Alípio Jorge Anália Lourenço Arlindo Oliveira Arlo Randall B. Cristina Pelayo Christopher Henry Daniel Gayo David Posada Emilio S. Corchado Eugénio C. Ferreira Fernando Diaz-Gómez Gonzalo Gómez-López Isabel C. Rocha Jesús M. Hernández Jorge Vieira José Adserias José L. López José Luís Oliveira Juan M. Cueva Júlio R. Banga University of Salamanca (Spain) Universidad of Pablo de Olavide (Spain) LIAAD/INESC, Porto LA (Portugal) University of Minho (Portugal) INESC-ID, Lisboa (Portugal) University of California Irvine (USA) University of Oviedo (Spain) Argonne National Labs (USA) University of Oviedo (Spain) Univ. Vigo (Spain) University of Burgos (Spain) IBB/CEB, University of Minho (Portugal) University of Valladolid (Spain) UBio/CNIO, Spanish National Cancer Research Centre (Spain) IBB/CEB, University of Minho (Portugal) University of Salamanca (Spain) IBMC, Porto (Portugal) University of Salamanca (Spain) University of Salamanca (Spain) Univ. Aveiro (Portugal) University of Oviedo (Spain) IIM/CSIC, Vigo (Spain) VIII Kaustubh Raosaheb Patil Kiran R. Patil Lourdes Borrajo Luis M. Rocha Manuel J. Maña López Margarida Casal Maria J. Ramos Martin Krallinger Nicholas Luscombe Nuno Fonseca Oscar Sanjuan Paulo Azevedo Paulino Gómez-Puertas Pierre Balde Rui Camacho Rui Brito Rui C. Mendes Sara Madeira Ségio Deusdado Vítor Costa Organization Max-Planck Institute for Informatics(Germany) Biocentrum, DTU (Denmark) University of Vigo (Spain) Indiana University (USA) University of Huelva (Spain) University of Minho (Portugal) FCUP, University of Porto (Portugal) CNB, Madrid (Spain) EBI (UK) CRACS/INESC, Porto (Portugal) University of Oviedo (Spain) University of Minho (Portugal) University Autónoma de Madrid (Spain) University of California Irvine (USA) LIACC/FEUP, University of Porto (Portugal) University of Coimbra (Portugal) CCTC, University of Minho (Portugal) IST/INESC, Lisboa (Portugal) IP Bragança (Portugal) University of Porto (Portugal) Organizing Committee Miguel Rocha (Co-chairman) Florentino Fernández Riverola (Co-chairman) Juan F. De Paz Daniel Glez-Peña José P. Pinto Rafael Carreira Simão Soares Paulo Vilaça Hugo Costa Paulo Maia Pedro Evangelista Óscar Dias CCTC, Univ. Minho (Portugal) University of Vigo (Spain) University of Salamanca (Spain) University of Vigo (Spain) University of Minho (Portugal) University of Minho (Portugal) University of Minho (Portugal) University of Minho (Portugal) University of Minho (Portugal) University of Minho (Portugal) University of Minho (Portugal) University of Minho (Portugal) Contents Microarrays Highlighting Differential Gene Expression between Two Condition Microarrays through Heterogeneous Genomic Data: Application to Lesihmania infantum Stages Comparison . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Liliana López Kleine, Vı́ctor Andrés Vera Ruiz An Experimental Evaluation of a Novel Stochastic Method for Iterative Class Discovery on Real Microarray Datasets . . . Héctor Gómez, Daniel Glez-Peña, Miguel Reboiro-Jato, Reyes Pavón, Fernando Dı́az, Florentino Fdez-Riverola 1 9 Automatic Workflow during the Reuse Phase of a CBP System Applied to Microarray Analysis . . . . . . . . . . . . . . . . . . . . . . Juan F. De Paz, Ana B. Gil, Emilio Corchado 17 A Comparative Study of Microarray Data Classification Methods Based on Ensemble Biological Relevant Gene Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Miguel Reboiro-Jato, Daniel Glez-Peña, Juan Francisco Gálvez, Rosalı́a Laza Fidalgo, Fernando Dı́az, Florentino Fdez-Riverola 25 Data Mining and Data Integration Predicting the Start of Protein α-Helices Using Machine Learning Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Rui Camacho, Rita Ferreira, Natacha Rosa, Vânia Guimarães, Nuno A. Fonseca, Vı́tor Santos Costa, Miguel de Sousa, Alexandre Magalhães 33 X Contents A Data Mining Approach for the Detection of High-Risk Breast Cancer Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Orlando Anunciação, Bruno C. Gomes, Susana Vinga, Jorge Gaspar, Arlindo L. Oliveira, José Rueff 43 GRASP for Instance Selection in Medical Data Sets . . . . . . . . . Alfonso Fernández, Abraham Duarte, Rosa Hernández, Ángel Sánchez 53 Expanding Gene-Based PubMed Queries . . . . . . . . . . . . . . . . . . . . Sérgio Matos, Joel P. Arrais, José Luis Oliveira 61 Improving Cross Mapping in Biomedical Databases . . . . . . . . . . Joel Arrais, João E. Pereira, Pedro Lopes, Sérgio Matos, José Luis Oliveira 69 An Efficient Multi-class Support Vector Machine Classifier for Protein Fold Recognition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wieslaw Chmielnicki, Katarzyna Sta̧por, Irena Roterman-Konieczna 77 Feature Selection Using Multi-Objective Evolutionary Algorithms: Application to Cardiac SPECT Diagnosis . . . . . . . António Gaspar-Cunha 85 Phylogenetics and Sequence Analysis Two Results on Distances for Phylogenetic Networks . . . . . . . . Gabriel Cardona, Mercè Llabrés, Francesc Rosselló 93 Cramér Coefficient in Genome Evolution . . . . . . . . . . . . . . . . . . . . 101 Vera Afreixo, Adelaide Freitas An Application for Studying Tandem Repeats in Orthologous Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 José Paulo Lousado, José Luis Oliveira, Gabriela Moura, Manuel A.S. Santos Accurate Selection of Models of Protein Evolution . . . . . . . . . . . 117 Mateus Patricio, Federico Abascal, Rafael Zardoya, David Posada Scalable Phylogenetics through Input Preprocessing . . . . . . . . . 123 Roberto Blanco, Elvira Mayordomo, Esther Montes, Rafael Mayo, Angelines Alberto The Median of the Distance between Two Leaves in a Phylogenetic Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 Arnau Mir, Francesc Rosselló Contents XI In Silico AFLP: An Application to Assess What Is Needed to Resolve a Phylogeny . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 Marı́a Jesús Garcı́a-Pereira, Armando Caballero, Humberto Quesada Employing Compact Intra-Genomic Language Models to Predict Genomic Sequences and Characterize Their Entropy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 Sérgio Deusdado, Paulo Carvalho Biomedical Applications Structure Based Design of Potential Inhibitors of Steroid Sulfatase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151 Elisangela V. Costa, M. Emı́lia Sousa, J. Rocha, Carlos A. Montanari, M. Madalena Pinto Agent-Based Model of the Endocrine Pancreas and Interaction with Innate Immune System . . . . . . . . . . . . . . . . . . . . . 157 Ignacio V. Martı́nez Espinosa, Enrique J. Gómez Aguilera, Marı́a E. Hernando Pérez, Ricardo Villares, José Mario Mellado Garcı́a State-of-the-Art Genetic Programming for Predicting Human Oral Bioavailability of Drugs . . . . . . . . . . . . . . . . . . . . . . . . 165 Sara Silva, Leonardo Vanneschi Pharmacophore-Based Screening as a Clue for the Discovery of New P-Glycoprotein Inhibitors . . . . . . . . . . . . . . . . . 175 Andreia Palmeira, Freddy Rodrigues, Emı́lia Sousa, Madalena Pinto, M. Helena Vasconcelos, Miguel X. Fernandes Bioinformatics Applications e-BiMotif: Combining Sequence Alignment and Biclustering to Unravel Structured Motifs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181 Joana P. Gonçalves, Sara C. Madeira Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in Escherichia Coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 Sónia Carneiro, Silas G. Villas-Bôas, Isabel Rocha, Eugénio C. Ferreira Rbbt: A Framework for Fast Bioinformatics Development with Ruby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201 Miguel Vázquez, Rubén Nogales, Pedro Carmona, Alberto Pascual, Juan Pavón XII Contents Analysis of the Effect of Reversibility Constraints on the Predictions of Genome-Scale Metabolic Models . . . . . . . . . . . . . . 209 José P. Faria, Miguel Rocha, Rick L. Stevens, Christopher S. Henry Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment . . . . . . . . . . 217 Paulo Maia, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha Genome Visualization in Space . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225 Leandro S. Marcolino, Bráulio R.G.M. Couto, Marcos A. dos Santos A Hybrid Scheme to Solve the Protein Structure Prediction Problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233 José C. Calvo, Julio Ortega, Mancia Anguita Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
